Root Genomics and Soil Interactions E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 736

Veröffentlichungsjahr: 2012

Beschreibung

Fully integrated and comprehensive in its coverage, Root Genomics and Soil Interactions examines the use of genome-based technologies to understand root development and adaptability to biotic and abiotic stresses and changes in the soil environment. Written by an international team of experts in the field, this timely review highlights both model organisms and important agronomic crops. Coverage includes: novel areas unveiled by genomics research basic root biology and genomic approaches applied to analysis of root responses to the soil environment. Each chapter provides a succinct yet thorough review of research.

Leseprobe

Contents

Cover

Title Page

Copyright

Contributors

Preface

Roots and Their Soil Interactions: What We Can Learn from Genomics

Chapter 1: Genomics of Root Development

Introduction

Genomics of LRI

Rise of New Technologies to Understand Lateral Root Development

ComparativOmics, the Future

Acknowledgments

References

Chapter 2: The Complex Eukaryotic Transcriptome: Nonprotein-Coding RNAs and Root Development

Genomic Approaches Reveal Novel Aspects of the Eukaryotic Transcriptome

The Role of RNA-Binding Proteins in npcRNA Metabolism and Activity

Nonprotein-Coding RNAs in Root Development

Future Perspectives

Acknowledgments

References

Chapter 3: Genomics of Auxin Action in Roots

Introduction

The Basis of Auxin Biology

Auxin Genomics in Root Development

Auxin and Root Hair Development

Auxin in Gravitropism

Auxin in LR Initiation

Conclusion

Acknowledgments

References

Chapter 4: Cell-Type Resolution Analysis of Root Development and Environmental Responses

Introduction

Tools for Cell-Type Resolution Analysis

Analysis of Spatiotemporal Expression Patterns in the Arabidopsis Root

Analysis of Cell-Type-Specific Expression Patterns in the Rice Root

Cell-Type-Specific Analysis of Auxin

Cell-Type-Specific Analyses of Chromatin

Cell-Type-Specific Analyses of Responses to Environmental Change

Future Prospects

Acknowledgments

References

Chapter 5: Toward a Virtual Root: Interaction of Genomics and Modeling to Develop Predictive Biology Approaches

Introduction

Assembling Root Gene Regulatory Pathways Using Genomics

Modeling Well-Characterized Small Root Gene Regulatory Networks

Building New Large-Scale Root Gene Regulatory Network

Multi-Scale Modeling Approaches to Study Root Growth and Development

Conclusions and Future Challenges

References

Chapter 6: Genomics of Root Hairs

Genomics with Single Cells

Root Hair Development

High-Throughput Approaches for the Characterization of Root Hairs

Functions of Root Hair-Specific Genes

The Regulatory Pathway for Root Hair-Specific Genes

Perspective

Acknowledgments

References

Chapter 7: The Effects of Moisture Extremes on Plant Roots and Their Connections with Other Abiotic Stresses

Introduction

Low Water Availability—Drought

Excess Water—Soil Waterlogging, Flooding, and Submergence

Common Plant Root Responses to Abiotic Stressors

Continuing Challenges in Breeding for Plant Root Systems Tolerant to Abiotic Stress

Acknowledgments

References

Chapter 8: Legume Roots and Nitrogen-Fixing Symbiotic Interactions

Genetic Dissection of the Legume Root System

Functional Genomic Analyses of Legume Nodules and Roots

Concluding Remarks

Acknowledgments

References

Chapter 9: What the Genomics of Arbuscular Mycorrhizal Symbiosis Teaches Us about Root Development

Forward and Reverse Genetics for Identifying Myc Mutants

Comparative Transcriptomics of AM Symbiosis: Toward Identification of Genes Involved in Root Development

Small RNAs in AM Symbiosis

Acknowledgments

References

Chapter 10: How Pathogens Affect Root Structure

Introduction

Root Infection and Feeding Cell Ontogenesis

Genome-Wide Analysis of the Plant Response to Infection

The Plant Cytoskeleton Is Targeted by Root Pathogens

Root Pathogens Hijack Cell Cycle Regulators

Severe Cell Wall Remodeling Is Associated with Feeding Site Formation

Phytohormones Regulating Development and Defense May Control Feeding Site Formation

Role of miRNAs in Feeding Site Formation and Function

Nematode Effectors That Alter Root Cell Development during Parasitism

Conclusion

Acknowledgments

References

Chapter 11: Genomics of the Root–Actinorhizal Symbiosis

Introduction

Actinorhizal Symbiosis

Development of Actinorhizal Nodules

Genomic Resources for Studying Actinorhizal Symbiosis

What Did We Learn from Actinorhizal Genomics?

Conclusion and Future Directions

Acknowledgments

References

Chapter 12: Plant Growth Promoting Rhizobacteria and Root Architecture

Introduction

Different Root Niches for PGPR Colonization

PGPR Recognition by Plants

Modulation of Root Growth and Architecture by PGPRs

Mechanisms of Plant Growth Promotion by PGPRs

Plant Genetic Programs Controlling Modulation of Root Growth and Architecture by PGPRs

Conclusions

Acknowledgments

References

Chapter 13: Translational Root Genomics for Crop Improvement

Introduction

Root Research for Crop Improvement

Genetic Dissection of Root Traits

Molecular Dissection of Root Traits

Molecular Breeding for Root Traits

Summary and Outlook

Acknowledgments

References

Index

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Library of Congress Cataloging-in-Publication Data

Root genomics and soil interactions / editor, Martin Crespi.   p. cm.  Includes bibliographical references and index.  ISBN 978-0-470-96043-1 (hardback : alk. paper) 1. Roots (Botany)–Physiology. 2. Roots (Botany)–Development. 3. Plant genomes. 4. Genomics. 5. Plant-soil relationships. I. Crespi, Martin.  QK644.R6523 2012  575.5′4–dc23

2012021109

A catalogue record for this book is available from the British Library.

Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books.

Contributors

Pierre AbadINRA-CNRS-Université de Nice Sophia-Antipolis Interactions Biotiques et Santé Végétale Sophia Antipolis, FranceNicole AlloisioCentre National de la Recherche Scientifique Ecologie Microbienne Université de Lyon Cedex Villeurbanne, FranceF. ArielInstitut des Sciences du Végétal Centre National de la Recherche Scientifique Gif sur Yvette cedex, FranceLeah BandCentre for Plant Integrative Biology University of Nottingham United KingdomF. BardouInstitut des Sciences du Végétal Centre National de la Recherche Scientifique Gif sur Yvette cedex, FranceThomas BaumDepartment of Plant Pathology and Microbiology Iowa State University Ames, Iowa, USATom BeeckmanDepartment of Plant Systems Biology and Department of Plant Biotechnology and Genetics Ghent University Ghent, BelgiumMalcolm BennettCentre for Plant Integrative Biology University of Nottingham United KingdomDidier BoguszEquipe Rhizogenèse Institut de Recherche pour le Développement Montpellier, FranceThais L.G. CarvalhoLaboratório de Biologia Molecular de Plantas Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Rio de Janeiro, BrazilSiva K. ChamarthiInternational Crops Research Institute for the Semi-Arid Tropics Hyderabad, IndiaHyung-Taeg ChoDepartment of Biological Sciences and Genomics and Breeding Institute Seoul National University Seoul, KoreaMartin CrespiInstitut des Sciences du Végétal Centre National de la Recherche Scientifique Gif sur Yvette cedex, FranceIsabelle DamianiINRA-CNRS-Université de Nice Sophia-Antipolis Interactions Biotiques et Santé Végétale Sophia Antipolis, FrancePierre-Marc DelauxLaboratoire de Recherche en Sciences Végétales Université de Toulouse Castanet-Tolosan, FranceJosé R. DinnenyCarnegie Institution for Science Department of Plant Biology Stanford, California, USA and Temasek Lifesciences Laboratory Department of Biological Sciences National University of Singapore SingaporeBruno FaveryINRA-CNRS-Université de Nice Sophia-Antipolis Interactions Biotiques et Santé Végétale Sophia Antipolis, FrancePaulo C.G. FerreiraLaboratório de Biologia Molecular de Plantas Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Rio de Janeiro, BrazilDamien FormeyLaboratoire de Recherche en Sciences Végétales Université de Toulouse Castanet-Tolosan, FranceFlorian FrugierInstitut des Sciences du Végétal (ISV), CNRS Gif-sur-Yvette cedex, FrancePooran M. GaurInternational Crops Research Institute for the Semi-Arid Tropics Hyderabad, IndiaAdriana S. HemerlyLaboratório de Biologia Molecular de Plantas Instituto de Bioquímica Médica Universidade Federal do Rio de Janeiro Rio de Janeiro, BrazilTarek HeweziDepartment of Plant Pathology and Microbiology Iowa State University Ames, Iowa, USAValérie HocherEquipe Rhizogenèse Institut de Recherche pour le Développement Montpellier, FranceCyril JourdaLaboratoire de Recherche en Sciences Végétales Université de Toulouse Castanet-Tolosan, FranceL. KrishnamurthyInternational Crops Research Institute for the Semi-Arid Tropics Hyderabad, IndiaLaurent LaplazeEquipe Rhizogenèse Institut de Recherche pour le Développement Montpellier, France and Laboratoire Commun de Microbiologie Centre de Recherche de Bel Air Dakar, SénégalPhilippe LaporteLaboratoire des Interactions Plantes Micro-organismes (LIPM) UMR CNRS-INRA Castanet-Tolosan Cedex, FranceJulien LavenusCentre for Plant Integrative Biology University of Nottingham United Kingdom and Institut de Recherche pour le Développement UMR DIADE Montpellier, FranceMikael LucasCentre for Plant Integrative Biology University of Nottingham United Kingdom and Institut de Recherche pour le Développement UMR DIADE Montpellier, FranceAlistair MiddletonCentre for Plant Integrative Biology University of Nottingham United Kingdom and Center for Biological Systems Analysis Albert-Ludwigs-Universität Freiburg, GermanyA.B. MorenoInstitut des Sciences du Végétal Centre National de la Recherche Scientifique Gif sur Yvette cedex, FranceHenry T. NguyenDivision of Plant Sciences University of Missouri Columbia, Missouri, USA and The National Center for Soybean BiotechnologyAndreas NiebelLaboratoire des Interactions Plantes Micro-organismes UMR CNRS-INRA Castanet-Tolosan Cedex, FrancePhilippe NormandCentre National de la Recherche Scientifique Ecologie Microbienne Université de Lyon Cedex Villeurbanne, FranceBoris ParizotDepartment of Plant Systems Biology and Department of Plant Biotechnology and Genetics Ghent University Ghent, BelgiumMichaël QuentinINRA-CNRS-Université de Nice Sophia-Antipolis Interactions Biotiques et Santé Végétale Sophia Antipolis, FranceReyazul Rouf MirInternational Crops Research Institute for the Semi-Arid Tropics Hyderabad, IndiaChristophe RouxLaboratoire de Recherche en Sciences Végétales Université de Toulouse Castanet-Tolosan, FranceIve De SmetDivision of Plant and Crop Sciences School of Biosciences University of Nottingham Loughborough, United KingdomMahendar ThudiInternational Crops Research Institute for the Semi-Arid Tropics Hyderabad, IndiaRajeev K. VarshneyInternational Crops Research Institute for the Semi-Arid Tropics Hyderabad, India and CGIAR-Generation Challenge Programme DF, Mexico and School of Plant Biology Faculty of Natural and Agricultural Sciences The University of Western Australia Crawley, WA, AustraliaLaura M. VaughnDivision of Plant Sciences University of Missouri Columbia, Missouri, USA and The National Center for Soybean Biotechnology and Department of Natural Resources and Environmental Sciences University of IllinoisElisabeth L. WilliamsDivision of Plant and Crop Sciences School of Biosciences University of Nottingham Loughborough, United KingdomMichael WilsonCentre for Plant Integrative Biology University of Nottingham United Kingdom

Preface

Roots and Their Soil Interactions: What We Can Learn from Genomics

Developmental plasticity allows higher organisms to adapt to their environment. In contrast to animals, plants exhibit a remarkable flexibility in their architecture and growth pattern in response to external conditions, due to the continuously active shoot and root meristems and their capability to generate new organs after embryogenesis. External cues influence plant growth by modulating hormone levels and signaling. The root architecture of the plant constitutes an important model to study how developmental plasticity is translated into growth responses under different soil conditions and plays an important role in water and nutrient acquisition. Indeed, primary root development and the formation of de novo meristems to generate lateral roots are conditioned by the soil environment. Lateral root growth and development is the main determinant of the shape of the root system, a trait controlled by internal cues and external factors. In addition to Arabidopsis, there are other relevant models where genomic information is becoming available, notably cereals and legumes. Both plants are able to develop symbiotic interactions with soil organisms, namely, mycorrhizal fungi and, for legumes, soil rhizobia. These interactions lead to further adaptation of root growth, the so-called mycorrhizal roots, and even to the formation of new organs, distinct from lateral roots, the nitrogen-fixing root nodules.

The diversity of root responses to biotic and abiotic stresses as well as symbiotic interaction can be analyzed at a genome-wide scale using transcriptomic and proteomic approaches. The advent of genomic technologies will open new perspectives for the analysis of how roots adapt to the soil environment. This work, mainly done in model systems such as Arabidopsis, uncover diverse regulatory genes (e.g., environmental sensors, protein kinases, transcription factors, and more recently, small regulatory RNAs) that participate in genetic programs, regulating root growth and architecture. Integration of these data with genomic approaches on different genetic backgrounds has already revealed, and will continue to reveal, critical regulatory networks and molecular hubs, whose orthologs could then be analyzed in crop plants to establish the generality of these mechanisms and impact agricultural practices.

This book contains 13 chapters from recognized experts in the field, which provide a comprehensive and integrated view of how root genomics can open new perspectives for root physiology and agriculture. The first six chapters deal with various novel areas where genomics, in combination with modeling, physiology, in-depth analysis of the transcriptome, and epigenetics, have revealed several regulatory networks controlling diverse aspects of root growth and development. Then, the remaining chapters describe genomic approaches being applied for the analysis of root responses to the soil environment, such as abiotic stresses, symbiotic interactions, or pathogenic nematode infections. The final chapter focuses on translational genomics and how genomics can guide crop improvement. I hope that this book will serve many, from plant researchers to plant and crop physiologists, breeders, graduate students, and their professors who want to have an overview of the highlights in root genomics and how this information could be screened and integrated without having considerable expertise in bio-statistics. While reading this book, the reader will realize how fascinating the actual global view of the genome is and how many complex mechanisms remain to be discovered to understand root growth and development. There are exciting agricultural challenges, such as the modulation of root architecture or drought adaptation, which may derive from the application of this new fundamental understanding of life principles to the control of major root traits.

Martin Crespi

1 Genomics of Root Development

Boris Parizot and Tom Beeckman

Introduction

Roots: Rising from the Underground

Because of the different roles the root system plays in overall plant growth, root architecture is a fundamental aspect of plant growth and development. The root system especially acquires water and nutrients from the soil, anchors the plant in the substrate, synthesizes hormones and metabolites, interacts with symbiotic microorganisms, and insures storage functions. In light of these characteristics, more and more breeders turn their attention to this underground organ in order to increase yield. This requires a better understanding of the relation of this part of the plant with the environment and of its highly adaptive behavior (Lynch 2007; Gewin 2010; Den Herder et al. 2010).

Within the angiosperms, major differences in root architecture between dicotyledonous and monocotyledonous plants exist. Dicots develop a tap root system composed of a main primary root, already formed during embryogenesis, which grows vertically into the soil and gives rise to the emergence of numerous lateral roots extending the surface area. Monocots have a fibrous root system in which the embryonic primary root is only important for the early development of the plant (Feix et al. 2002) and in which an extensive postembryonic shoot-born root system is formed later on. Very little is known about the genetic and molecular mechanisms involved in the development and architecture of the root system in major crop species, generally monocotyledonous plants. Lack of insight is certainly a consequence of the difficulty to access and observe this organ in its natural habitat, namely the soil. Moreover, and probably because of this hidden character, the root has been neglected for a long time in crop improvement and in agricultural approaches aiming at increasing shoot biomass. Nevertheless, while most of the work has been done on Arabidopsis thaliana, the awareness of the importance of the root system in modulating plant growth, together with progress in sequencing and new molecular techniques, has caused renewed interest in understanding molecular mechanisms in crop species (Hochholdinger and Zimmermann 2009; Coudert et al. 2010).

In the scope of root development and its interaction with the soil, in this chapter, we propose to focus on the mechanisms involved in root branching, which is a major determinant of root system architecture. The plasticity of the root system represents indeed an important potential for plants, being sessile organisms, to adapt to the heterogeneity of their environment. The soil is a complex mixture of solid, gaseous, and liquid phases, wherein nutrients are unequally distributed. Plants have therefore developed a highly sophisticated regulatory system to control their root architecture, in response to environmental cues, by modulating intrinsic pathways to optimize their root distribution in the soil and consequently guarantee an optimal uptake of nutrients necessary for growth and development (reviewed in Croft et al. 2012).

Primary Root Structure and Development: Lessons from the Arabidopsis Model

Branching of roots occurs through the development of new meristems inside the primary parent root. We therefore first discuss briefly the structure and development of the primary root in Arabidopsis, the model species in which major insights were obtained, thanks to its simple root architecture (Dolan et al. 1993; Malamy and Ryan 2001; Scheres et al. 2002; Casimiro et al. 2003; Casson and Lindsey 2003; Ueda et al. 2005; Iyer-Pascuzzi et al. 2009; Peret et al. 2009).

The root can be divided in three main zones. The most distal, at the tip of the root, is the meristematic zone, where the so-called initial cells give rise to the tissues constituting the root. The initial cells are kept in an undifferentiated state by the neighboring quiescent center (Van den Berg et al. 1997), a mitotically less active region, composed of few central cells in Arabidopsis. Higher up, in the elongation zone, cells progressively stop dividing and start to expand longitudinally. Finally, cells differentiate and acquire their final cell fate in the maturation zone (Truernit et al. 2006), which can be recognized by the appearance of the anatomical structures of the vascular tissues.

Distinct cell types are then composing the mature root (Figure 1.1). The outer layers, endodermis, cortex, and epidermis are organized in concentric layers and present a radial organization toward the longitudinal axis of the primary root (Dolan et al. 1993). The epidermis, which is the outermost layer of the root, is in direct contact with the soil and is often designated as rhizodermis. It is composed of two populations of cells: one producing root hairs and the other nonhair cells (Schneider et al. 1997). The root hairs are responsible for the major part of the nutrient uptake from the soil (Muller and Schmidt 2004) and also play other important roles such as the initial contact with certain symbiotic partners (Gilroy and Jones 2000; Perrine-Walker et al. 2011). Cortex and endodermis constitute the ground tissue and are derived from one single initial cell in Arabidopsis (Dolan et al. 1993; Scheres et al. 1994). The stele is situated internal to these layers and comprises the vascular cylinder, consisting of two bilateral poles of xylem alternating with two bilateral poles of phloem separated by procambium cells (Dolan et al. 1993). The stele also contains a heterogeneous layer, the pericycle, interfacing the vascular cylinder and the outer layers, playing a predominant role in root architecture and root branching (Parizot et al. 2008).

FIGURE 1.1 Structure of the primary root and different steps of lateral root initiation. See the text for detailed description.

Root Branching

In dicotyledonous plants, such as Arabidopsis, elaboration of the root system occurs postembryonically by the formation of numerous secondary roots from the primary root that was formed during embryogenesis. These new roots are comparable to the primary root in structure and will be able to reiterate the branching process by in turn initiating tertiary roots. Roots of second, third, and higher order are defined as lateral roots. The plant can also produce adventitious roots, which initiate mostly at the base of the hypocotyl. Different markers related with cell identity show a similar pattern in the primary and lateral roots (Malamy and Benfey 1997b; Laplaze et al. 2005), indicating the possibility of a common developmental pathway. This hypothesis is supported by a high number of mutants affected in genes involved in root patterning, such as SHORTROOT, SCARECROW, and LONESOME HIGHWAY, showing similar defects in the primary and lateral roots (Helariutta et al. 2000; Wysocka-Diller et al. 2000; Parizot et al. 2008; Lucas et al. 2011). However, some differences can be observed in the behavior of the primary and the lateral roots toward external cues such as gravity and substrate nutrient concentrations (Zhang and Forde 1998; Mullen and Hangarter 2003; Bai and Wolverton 2011). A mutation in the gene MONOPTEROS impairs the apical–basal pattern formation of the embryo and leads to plants lacking a primary root, but that are still able to generate adventitious roots (Berleth and Jurgens 1993; Przemeck et al. 1996), indicating that early pathway(s) required for the embryonic formation of a root meristem are not required postembryonically. Also, a mutation in the gene WOODEN LEG has a major effect on the primary root development, with the suppression of the phloem elements and a drastic reduction in lateral root initiation (LRI), but does not affect the formation and branching of adventitious roots (Kuroha et al. 2006).

The monocots, such as maize, form different types of roots: primary, seminal, and adventitious roots, which can all form lateral roots. These root types also present similarities in their structures. However, mutants missing only a subset of these root types have been isolated, indicating that at least a part of the genetic program necessary for their formation is root-type specific (Woll et al. 2005; Hochholdinger and Tuberosa 2009).

Lateral Root Initiation

In Arabidopsis and most other dicotyledonous plants, lateral roots are formed from a restricted number of pericycle cells located in front of the xylem poles (Figure 1.1). The pericycle is a heterogeneous tissue composed of quiescent cells adjacent to the phloem poles and cells competent for LRI in front of the xylem poles (Beeckman et al. 2001; Parizot et al. 2008). Therefore, this layer presents a radial bilateral symmetry along the primary root, which reflects the diarch symmetry of the more internal vascular bundle as compared to the surrounding concentric radial layers of the outer tissues. The subpopulation of pericycle cells adjacent to the xylem poles can be considered as an extended meristem, as they conserve the ability to divide after leaving the root apical meristem (in contrast to the cells in front of the phloem poles), and give rise to the formation of a new organ (Beeckman et al. 2001; Casimiro et al. 2003). Although up to three adjacent pericycle cell files associated with each xylem pole are dividing during lateral root formation, cell lineage experiments have shown that only the central cell file will contribute significantly to the formation of the lateral root primordium (Kurup et al. 2005).

The first pericycle cell divisions that will give rise to a lateral root (i.e., formative divisions) can only be detected several millimeters above the primary root meristem, whereas in the lower part of a region named developmental window (Dubrovsky et al. 2006), it has been demonstrated that a subset of pericycle cells is already specified for LRI in a zone situated immediately above the primary root apical meristem, the basal meristem (De Smet et al. 2007; De Rybel et al. 2010b). The phytohormone auxin is most likely the signal triggering this priming, as auxin response recorded using the auxin response marker DR5 shows pulsations in the protoxylem cells of the basal meristem with a periodicity that can be correlated with the initiation of new lateral roots (Ulmasov et al. 1997; De Smet et al. 2007; De Rybel et al. 2010b; Moreno-Risueno et al. 2010). Up to now, different hypotheses have been proposed to explain the origin of these oscillating auxin response maxima in the protoxylem cells, and no consensus has been reached yet. Also the mechanism by which this auxin signal in the protoxylem cells is translated into the specification of founder cell identity in the neighboring pericycle cells is still unknown. Nevertheless, this intrinsic mechanism can be overruled, as the application of auxin on mature parts of the root above the basal meristem is still able to trigger LRI (Himanen et al. 2002), further reflecting the high plasticity of the root system.

The first morphological event preceding the division of two adjacent pericycle founder cells is the simultaneous migration of their nuclei to their common cell wall (De Smet et al. 2007). This migration is followed by an asymmetric anticlinal division of the pericycle cells, resulting in the formation of a core of small daughter cells flanked by larger cells (Dubrovsky et al. 2000). Successive anticlinal and periclinal divisions give rise to a lateral root primordium. Further divisions and elongation of the primordium cells result in the formation of a fully autonomous root, with a meristem similar to that of the primary root (Malamy and Benfey 1997b; Dubrovsky et al. 2001). Although the place of LRI differs between plant species, early patterning of the primordium is quite conserved (Casero et al. 1995; Malamy and Benfey 1997bb). The frequency of LRI in the Arabidopsis primary root can fluctuate in response to tropic and/or mechanical stimuli (De Smet et al. 2007; Ditengou et al. 2008; Laskowski et al. 2008; Lucas et al. 2008a). For example, a gravitropic stimulus applied to seedlings induces a lateral root at the place where the root bends to recover its normal growth angle (Lucas et al. 2008a).

Genomics of LRI

Most of the work on root development focused on the analysis of single mutants and allowed the discovery of many processes involved in the patterning of the different cell types within the primary root and in LRI. These studies show that root growth and development are complex processes with intricate pathways dealing with hormone biosynthesis, transport and signaling, tissue differentiation and dedifferentiation, nutrient sensing, cell divisions, and others (Iyer-Pascuzzi and Benfey 2009; Orman et al. 2011).

LRI has been increasingly studied over the last decade in the light of transcriptomics and proteomics. Material extraction for these analyses evolved from simple global root harvesting to more elaborated sampling techniques allowing a specific access to the tissues involved, such as laser capture microscopy (LCM; Woll et al. 2005) or cell sorting (De Smet et al. 2008). Also, the possibility to synchronize LRI circumvented the problems due to the discreteness of this event in plants grown in natural conditions (Himanen et al. 2002; Himanen et al. 2004). Different large-scale transcriptome and proteome studies have therefore been realized in different species, mainly Arabidopsis and maize, yielding information on various aspects of this de novo organogenesis: auxin response, asymmetric cell division, and pericycle tissue involvement. While these studies focused initially on the onset of lateral root development, a new era initiates now with the study of the formation and the patterning of the primordium after LRI and the emergence of the primordia from the parent root. Moreover, many other experiments are dealing with mechanisms related to LRI, such as meristem function, pericycle identity, and hormone treatment, and bring useful novel information, shedding light on this process. A list of omics experiments, directly or indirectly related to LRI is displayed in Table 1.1. A challenging task for the community will be to handle this wealth of data and search for appropriate system biology strategies to better understand the LRI process at the molecular level. To address this, a common effort of the biologists and the bioinformaticians is needed to design better experiments, rationalize and interpret the data, and make it accessible and understandable for the community. The most often characterized process in relation to LRI is the response to the hormone auxin.

Table 1.1 Omics Experiments dealing directly or indirectly with lateral root initiation. Publication year and reference, species, technique and experimental design, platform, tissues and preparation, pathways, treatments, and the biological process questioned by the experiment.

IAA Proteins

Although little is known on the origin of the signals triggering the auxin maximum, which induces the priming of the pericycle cells or the migration of the nuclei leading to LRI, much more is known about the downstream auxin transduction pathways (Fukaki et al. 2007).

One of the first components of this pathway is IAA14/SOLITARYROOT1 (SLR1), a member of the Aux/IAA gene family (Fukaki et al. 2002). Aux/IAA proteins are short-living nuclear proteins, most of which are induced early by auxin and act as active repressors of gene transcription. Accumulation of auxin causes the degradation of Aux/IAA proteins. Aux/IAA proteins are present all over the plant kingdom (Table 1.2). They are already described in monocots such as maize and rice (Jain et al. 2006; Wang et al. 2010b) and in dicots such as poplar (Kalluri et al. 2007), but are not found in animals (Riechmann et al. 2000). In the presence of auxin, Aux/IAA proteins bind to the F-box proteins TIR1, AFB1, 2, and 3 (Dharmasiri et al. 2005; Kepinski and Leyser 2005) and become targeted to the ubiquitin-dependent proteasome-degrading pathway (Zenser et al. 2001; Gray et al. 2003). Regulation of plant auxin sensitivity can be modulated by the control of TIR1 expression levels as it is the case during phosphate nutrient deprivation. Phosphate deprivation increases the expression of TIR1 and consequently causes Aux/IAA auxin response repressors to be degraded and LRI to be induced in Arabidopsis seedlings (Perez-Torres et al. 2008). Also, nitric oxide was recently shown to enhance TIR1–Aux/IAA interaction, which can explain how nitric oxide depletion blocks Aux/IAA protein degradation (Terrile et al. 2012).

Table 1.2 Plaza 2.5 output of LRI-related homologous genes in plant kingdom. The number of genes for each species and in each family corresponds to the result of a bioinformatics algorithm (http://bioinformatics.psb.ugent.be/plaza/). These results can be slightly different from the curated number of genes presented in the literature.

A single point mutation in the conserved amino acid core sequence “GWPPV” in domain II of Aux/IAA proteins was shown to stabilize them (Ramos et al. 2001), leading to gain-of-function mutants. In the case of IAA14/SLR1, the resulting gain-of-function mutant slr-1 fails to initiate formative divisions in the pericycle founder cells and consequently does not develop any lateral roots (Fukaki et al. 2002). Other gain-of-function mutants of some Aux/IAA gene family members, IAA1/AXR5, IAA3/SHY2, IAA18/CRANE, IAA19/MSG2, and IAA28, also show strong lateral root development phenotypes (Tian and Reed 1999; Rogg et al. 2001; Tatematsu et al. 2004; Yang et al. 2004; Uehara et al. 2008), indicating their involvement in this process. Nevertheless, none of these mutants totally block LRI as in the case of slr-1.

In addition, the loss-of-function iaa14-1 mutant does not show any obvious phenotype (Okushima et al. 2005), as it is also the case for other loss-of-function iaa mutants (Rouse et al. 1998; Fukaki et al. 2002; Uehara et al. 2008), indicating a possible redundancy in the function of Aux/IAA genes. Recently, it was demonstrated that an OsIAA11 gain-of-function mutation caused the inhibition of lateral root development in rice (Zhu et al. 2011). Interestingly, on the basis of protein sequence, OsIAA11 is one of the closest homologs of IAA14 in Arabidopsis (Jain et al. 2006). Nevertheless, the mutation in OsIAA11 is semidominant for lateral root development, and the mutant phenotype differs from that of Arabidopsisiaa14-1, indicating that the auxin regulation pathways mediated by these two genes might be different (Zhu et al. 2011).

To unravel the pathways leading to the formative divisions downstream of SOLITARY ROOT (SLR), a comparative analysis was realized between the slr-1 mutant and the wild type using the lateral root-inducible system (LRIS; Vanneste et al. 2005). It was observed that the mutation affected a number of cell cycle regulatory genes. The authors overexpressed the cell cycle regulator CYCD3;1 (which promotes G1 to S phase transition) in the slr-1 background to rescue its rootless phenotype. Though inducing a few rounds of anticlinal divisions, this strategy failed in the formation of lateral root primordia, indicating that cell cycle activation in the pericycle cells of the mutant slr-1 is not sufficient to get formative divisions and proper LRI (Vanneste et al. 2005).

Auxin Response Factor Transcription Factors

Auxin response factors (ARFs) are transcription factors that act as repressors, except for a few of them (ARF4, 5, 6, 7, and 19) (Tiwari et al. 2003; Tiwari et al. 2004). They dimerize with Aux/IAA proteins (Guilfoyle and Hagen 2007), are present in most plant kingdom species (Table 1.2), are described in both monocots and dicots, such as rice and poplar (Wang et al. 2007; Kalluri et al. 2007), and are plant specific (Riechmann et al. 2000). The transcription factors NPH4/ARF7 and ARF19 have been shown to play a crucial role in LRI. They directly interact with IAA14/SLR, which causes their sequestration and prevents their positive transcriptional action (Fukaki et al. 2005). The degradation of IAA14/SLR leads to the release of these ARFs, which in turn activate the expression of their target genes. Consequently, the double mutant arf7 arf19 presents a drastic LRI phenotype very similar to slr-1 (Fukaki et al. 2002; Wilmoth et al. 2005). As this mutant is nevertheless still able to initiate some discrete roots, other ARFs may also be involved in this process (Fukaki et al. 2007).

A transcriptome experiment was performed to dissect further the SLR/ARF7/ARF19 pathway by comparing gene regulation upon auxin treatment in the mutants arf7 and arf19, and in the double mutant arf7 arf19 (Okushima et al. 2005). Several genes, which are not auxin-inducible anymore in the arf7 arf19 double mutant compared to the wild type, such as lateral organ boundaries domain (LBD) proteins, are also impaired in the slr-1 mutant background (Okushima et al. 2005; Vanneste et al. 2005). Among other results discussed in the next chapters, this observation indicates that even though the transcriptome experiment on the arf7 arf19 mutant was performed with whole seedlings, it brings important information about specific processes such as LRI and formation. The functional analysis of genes concomitantly showing up in these transcriptome experiments greatly helped in understanding how a stabilized version of IAA14 blocks LRI and how ARF7 and ARF19 activate it (Okushima et al. 2007). Another auxin module, composed of MONOPTEROS/ARF5 acting downstream of BODENLOS (BDL)/IAA12, was recently reported to be activated during LRI. Overexpression of MONOPTEROS is able to rescue the phenotype of the slr-1 mutant (De Smet et al. 2010), indicating that the auxin control on LRI is at least bimodal. It is most likely that other modules are involved in the control of root development as other ARFs have been shown to be implicated in adventitious and lateral roots (Tian et al. 2004; Mallory et al. 2005; Wang et al. 2005; Gutierrez et al. 2009).

Downstream of ARF Factors

LBD genes form a large family of plant-specific transcription factors that can be themselves the targets of ARF transcription factors. LBD genes are present all over the plant kingdom (Table 1.2) and are already described in dicots and monocots, such as Arabidopsis, maize, and rice (Yang et al. 2006; Taramino et al. 2007), but again do not exist in animals (Shuai et al. 2002). LBD16/ASYMMETRIC LEAVES2-LIKE18 (LBD16/ASL18) and LBD29/ASL16 appear to act immediately downstream of ARF7 and ARF19. They mediate auxin-regulated lateral root formation and their overexpression can rescue the arf7 arf19 double mutant phenotype (Okushima et al. 2007; Lee et al. 2009). LBD16 was recently shown to regulate the polar migration of the nucleus and the asymmetric division of the lateral root founder cells (Goh et al. 2012). CROWN ROOTLESS1/ADVENTITIOUS ROOTLESS1 (CRL1/ARL1), which is among the closest rice homologs of AtLBD16 and AtLBD29, presents a conserved role in root development and regulates the formation of lateral and adventitious roots (Inukai et al. 2005; Liu et al. 2005). Similarly, ROOTLESS CONCERNING CROWN AND SEMINAL ROOTS (RTCS) and RTCS-LIKE, which are also LBD proteins, are involved in the initiation and the formation of seminal and shoot-born roots in maize (Taramino et al. 2007).

Cell Cycle

LRI takes place above the differentiation zone, in a region of the root where cells hardly divide. The pericycle in front of the xylem poles makes an exception to this rule and divides asymmetrically to form a new lateral root. It was proposed, on the basis of cell cycle marker characterization and cell length measurements, that this peculiar behavior of the pericycle is insured by a particular mitotic status (Beeckman et al. 2001). Expression of the cyclin CYCA2;1 indicates the progression of the xylem pole pericycle cells toward the G2 phase of the cell cycle (Beeckman et al. 2001). The cyclin CYCB1;1 is expressed during the G2-M transition of the cell cycle, and because its transcription precedes the completion of cell division, it was selected and is now commonly used as a marker for LRI (Himanen et al. 2002; Himanen et al. 2004; Vanneste et al. 2005). Opposite to enhanced cell cycle progression at the xylem poles, expression of the cell cycle inhibitor KRP2 in the phloem pole pericycle cells indicates a blockage of these cells toward cell division (Himanen et al. 2002).

Several evidences indicate a role of the hormone auxin in the regulation of the cell cycle. Treatment of seedlings with N-1-naphthylphthalamic acid (NPA), which blocks the transport of auxin, triggers a general arrest of the cell cycle in the G1 phase and expression of KRP2 overall the pericycle (Himanen et al. 2002). Also, in the slr-1 mutant, cell division in the pericycle is blocked, indicating a link between SLR/IAA14-dependent auxin signaling and cell cycle activation in the pericycle prior to LRI (Fukaki et al. 2002; Vanneste et al. 2005).

Nevertheless, the particular cell cycle fate of the pericycle does not seem to be controlled only by auxin. The nuclear protein ALF4 is necessary to maintain the mitotic competence of the xylem pole pericycle. A mutation in this gene blocks LRI, as observed with the mitotic marker CYCB1;1 : GUS, and causes on the other hand an increase in expression of the earlier cell cycle marker CDKB;1 : GUS. ALF4 is however not induced by auxin and might therefore control pericycle meristematic identity independently of the canonical hormone pathways (DiDonato et al. 2004).

Asymmetric and Formative Divisions

Cell cycle activation is naturally occurring in the xylem pole pericycle cells and leads to several rounds of asymmetric cell divisions, characteristic of the generation of new cell fates or organs (Scheres and Benfey 1999; De Smet and Beeckman 2011). In many plant species, LRI starts with an asymmetric and formative division of the founder cells (Casero et al. 1993; Casero et al. 1995; Malamy and Benfey 1997a). This notion is fundamental: the pericycle of the tomato (Solanum lycopersicum) mutant diageotropica (dgt) undergoes several rounds of divisions, which are not formative and fails to develop proper lateral roots (Ivanchenko et al. 2006). Similarly in Arabidopsis, bypassing the division blockage in the slr-1 mutant by forcing cell cycle transition by means of CYCD3;1 overexpression gives a comparable phenotype, with stretches of pericycle cells undergoing proliferative divisions, but failing to form primordia (Vanneste et al. 2005).

A transcriptome experiment was performed especially to track regulation of gene expression occurring during the first asymmetric cell divisions of LRI. A transcript profiling of the xylem pole pericycle cells undergoing synchronous asymmetric divisions was performed making use of the LRIS in combination with cell sorting of the marker line J0121 (De Smet et al. 2008). Combining the list of genes significantly regulated during the treatment with previously published transcriptome experiments, the authors selected genes that are not involved in general cell cycle regulations, exception made for the G2-M phase transition (Menges et al. 2003), but which were already shown to be involved in LRI and to be dependent on the SLR/IAA14 auxin response pathway (Vanneste et al. 2005). This experiment allowed the discovery of the receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4), which is expressed in the small daughter cells during the first asymmetric divisions in the xylem pole pericycle. This receptor was demonstrated to promote formative cell divisions in the pericycle and, once organogenesis has been started, to constrain their occurrence in the core cells of the future primordium by preventing divisions of the neighboring pericycle cells (De Smet et al. 2008). A comparable double role has been described in leaf development for the maize homolog CRINKLY4/CR4 (Becraft et al. 2001).

In Arabidopsis, asymmetric cell division is preceded by an auxin accumulation in the founder cells (Benkova et al. 2003; Dubrovsky et al. 2008; De Rybel et al. 2010b), which triggers the characteristic migration of two adjacent cell nuclei toward their common cell wall (De Smet et al. 2007; De Rybel et al. 2010b). The correct migration of the nucleus is dependent on signaling cascades involving IAA28, SLR/IAA14, ARF7, ARF19, and LBD16, highlighting the importance of auxin signaling in this process (De Rybel et al. 2010b; Goh et al. 2012). These observations are related to the observations made in the gnom mutant. The protein GNOM is a regulator of the intracellular vesicle trafficking involved in the recycling of the PIN1 auxin transporter to the membrane (Geldner et al. 2003). gnom mutants fail to express the marker ACR4 and to initiate proper formative divisions (De Smet et al. 2008). Another observation emphasizing the role of auxin is the possibility to rescue the phenotype of the slr-1 plants overexpressing CYCD3;1 by auxin treatment, allowing to recover formative divisions and LRI (De Smet et al. 2010). Also recently, the transcription factor E2Fa was shown to be an essential component linking auxin pathways and asymmetric cell division triggering LRI. E2Fa expression is indeed regulated by the LBD18 / LBD33 dimer that is under direct control of the auxin-signaling pathway (Berckmans et al. 2011).

Digging into LRI, the Priming of the Pericycle

Although relatively much is discovered concerning the molecular pathways connecting the auxin signals driving the formative cell divisions of the pericycle and further lateral root development, very little is known on the origin of this signal and on the very early steps preceding LRI. Different hypotheses have been proposed to explain the origin of the recurrent auxin response oscillations observed in the basal meristem. One explanation would be that the auxin fluxes responsible for the gravitropic response in the root tip are driving LRI. Gravitropism and LRI are indeed coregulated in Arabidopsis (Lucas et al. 2008a). During gravitropic response, shoot-derived auxin is redistributed basipetally, relative to gravity, from the columella root cap cells to the epidermis cells, through the lateral root cap. Higher up in the region of the basal meristem, auxin is redirected to the stele by PIN1 and PIN2 transporters (Blilou et al. 2005; Leyser 2006; Ditengou et al. 2008). This feedback loop could explain the auxin response oscillations (Lucas et al. 2008b). A transcriptomic approach was recently performed to test the relationship between the auxin response maxima in the basal meristem and the control of root branching and bending (Moreno-Risueno et al. 2010). The authors tracked gene expression fluctuations in correlation to the auxin response oscillations and showed that these last ones were not sufficient to trigger the periodic specification of pericycle founder cells. This specification would rather be the consequence of the oscillating expression of transcription factors such as SHATTERPROOF1 and 2 (SHP1 and SHP2), SEEDSTICK (STK), and AGAMOUS-LIKE20 (AGL20) (Moreno-Risueno et al. 2010).

Another transcriptomic approach shed some light on the mechanisms involved in pericycle founder cells specification. The meta-analysis of different datasets related to LRI allowed the selection of genes that are differentially expressed between xylem and phloem pole pericycle cells, not expressed in other radial tissue layers, responsive to auxin, and that are predicted to have a role in asymmetric division but not in general cell-cycle phase transitions (De Rybel et al. 2010b; Parizot et al. 2010). Among the candidates, the authors characterized GATA23, a member of the GATA-type family of transcription factors that are known to have several regulatory roles in cell fate specification (Reyes et al. 2004). GATA23 is positively regulated by auxin treatment. It is expressed in a region above the basal meristem in correlation with the oscillating auxin response maxima, probably through an IAA28-controlled auxin response pathway, and induces founder cell identity (De Rybel et al. 2010b).

Apart from auxin, other hormones have been described to play an important role in LRI. LRI is inhibited in mutants with an increased level of ethylene (Nodzon et al. 2004; Ivanchenko et al. 2008; Prasad et al. 2010) and by abscisic acid treatment (De Smet et al. 2006). Cytokinins are known to inhibit LRI by blocking cell cycle progression in the founder cells and interfering with the auxin maxima (Li et al. 2006; Laplaze et al. 2007). Also, an increasing number of studies focus on the interplay of cytokinins with auxin pathways (Dello Ioio et al. 2008; Su et al. 2011; Zheng et al. 2011). Future experiments dedicated to this cross talk in relation to LRI should provide a lot of information on the synergies and antagonisms in these pathways (Duclercq et al. 2010). Furthermore, as it is the case for auxin, cytokinins are involved in multiple symbiotic processes (Hirsch et al. 1997; Barker and Tagu 2000; Lohar et al. 2004; Frugier et al. 2008). It has been shown that during symbiotic interactions, the bacteria can hijack the plant lateral root development program to form a nodule (Mathesius et al. 2000). The discovery of important genes commonly regulated in the different symbioses (Gherbi et al. 2008; Markmann et al. 2008), combined with histological similarities during development, such as divisions in the xylem pole pericycle (Péret et al. 2007), point to common regulatory mechanisms between lateral root and symbiotic nodule development pathways. Consequently, it may be valuable to compare these developmental processes at the transcriptomic or proteomic level, using published or upcoming datasets (Van Noorden et al. 2007; Benedito et al. 2008; Libault et al. 2010).

Primordium Patterning, Emergence, and Activation

A succession of stereotypic divisions accompanies the passage from pericycle founder cells to the emergence of a new lateral root through different well-characterized developmental stages (Malamy and Benfey 1997b). The first anticlinal and asymmetric divisions of the pericycle produce a single-layered primordium and are followed by periclinal divisions forming an inner and an outer layer. Further anticlinal and periclinal divisions yield a dome-shaped primordium that eventually emerges from the parent root and becomes autonomous. At this point, divisions of the different tissues formed in the primordium stop, and divisions of the initials cells that become responsible for root growth and elongation start (Malamy and Benfey 1997b).

In addition to its role in triggering LRI, auxin also plays an important role in the patterning and the emergence of the primordium. From the first stage on, an auxin gradient is formed in the central cells and is maintained in the tip of the primordium during its development (Benkova et al. 2003). Two-step models have been proposed for lateral root formation, and particularly for the establishment and the maintenance of this auxin gradient (Celenza et al. 1995; Laskowski et al. 1995; Sussex et al. 1995; Bhalerao et al. 2002). The AUX1 auxin influx carrier facilitates auxin uptake in the central core cells of the primordium as early as the first stage (Marchant et al. 2002). Later, when it reaches a size of about three to five cell layers, the primordium is able to synthesize its own auxin (Ljung et al. 2005). A combination of PIN polar auxin transport proteins helps in maintaining the gradient with a maximum at the tip. Mutations or mis-expression of these PIN proteins lead to abnormally shaped and/or nonemerged primordia (Benkova et al. 2003). It was recently shown that the nitrate transporter NRT1.1 not only transports nitrate but also facilitates auxin uptake in primordia and lateral roots, stimulating lateral root development and growth (Krouk et al. 2010). However, this NRT1.1-dependent auxin transport is inhibited by nitrate itself, defining another connection between nutrient and hormone signaling during organ development (Perez-Torres et al. 2008; Krouk et al. 2010). Downstream of auxin transport, the IAA14/SLR auxin response module was shown to be also involved during lateral root formation. Tissue-specific expression of a dominant negative form of the IAA14/SLR transcription factor in developing primordia leads to abnormal and/or arrested lateral root development (Fukaki et al. 2005).

Cytokinin hormones also play a crucial role in patterning the new lateral root primordium. Tissue-specific expression of a cytokinin biosynthesis gene, IPT (ISOPENTENYL TRANSFERASE) in the xylem pole pericycle, blocks lateral root patterning, especially by interfering with the correct expression of PIN genes and misleading a correct auxin gradient (Laplaze et al. 2007). Attempts to bypass this blockage by adding auxin to plants expressing IPT in the xylem pole pericycle, and therefore in the founder cells, caused cell proliferation but failed to induce the formation of patterned primordia. Cytokinin treatments of the root also perturb lateral root patterning and provoke abnormal and ectopic divisions, which give rise to a flattened primordium. However, the main effect of cytokinins appears to be prior to the formation of the primordium itself, as the expression of IPT in the developing primordium does not impair its development as much as in the case of earlier expression in the founder cells (Laplaze et al. 2007). Expression patterns of members of the IPT gene family are consistent with these observations; IPT3, which is expressed in the pericycle, presents higher expression in the phloem pole compared to the xylem pole pericycle, and IPT5 is expressed in young lateral root primordia (Miyawaki et al. 2004).

Next to its role in promoting formative cell divisions during early lateral root formation, ACR4 also plays a role in lateral root patterning. acr4 mutants present altered expression of the boundary marker LBD5 and an abnormal auxin gradient as seen with the DR5 marker (De Smet et al. 2008). ACR4 encodes a membrane-associated receptor kinase, which indicates the possibility of novel signaling molecules, such as peptides, regulating LRI and primordium patterning. This vision is supported by the cell division inhibitory potential of ACR4 on cells where it is not expressed, indicating probable regulation by a noncell-autonomous signal (De Smet et al. 2008). Similar to observations in acr4 mutants, mutation in the AP2 (APETALA2)/EREBP (ETHYLENE RESPONSIVE ELEMENT BINDING PROTEIN) transcription factor PUCHI leads to abnormal divisions in the lateral root primordium and ectopic divisions in the neighboring cells, giving rise to a flattened primordium (Hirota et al. 2007). Other genes belonging to CUP-SHAPED COTYLEDON and LOB (LATERAL ORGAN BOUNDARIES) gene families exhibit an expression pattern delineating the newborn organs. These families have been extensively described in the shoot of the plant and, among other roles, define the boundaries of emerging organs. Analogous expression patterns in the root suggest a similar role of these genes in restricting divisions in the cells neighboring the developing organ (Shuai et al. 2002; Vroemen et al. 2003; Laufs et al. 2004; Laplaze et al. 2005).

On its way to the outer world, the primordium still needs to overcome a last step, which consists in passing through the overlaying tissues, that is, endodermis, cortex, and epidermis. Although these tissues are composed of one layer of cells in Arabidopsis (Dolan et al. 1993), the cortex can be composed of up to 15 layers in other plant species such as maize (Hochholdinger et al. 2009). Recently, several cell wall remodeling (CWR) enzymes have been discovered in Arabidopsis, among which a pectate lyase (PLA2), a polygalacturonase (ADPG2), a pectin methyl-esterase (PME1), an expansin (EXP17), a xyloglucan:xyloglucosyl transferase (XTR6); and a glycosyl hydrolase (GLH17) are expressed in the overlaying tissues and most probably facilitate lateral root emergence by causing cell separation (Henrissat 1991; Neuteboom et al. 1999; Cosgrove 2000; Marin-Rodriguez et al. 2002; Vissenberg et al. 2005; Laskowski et al. 2006; González-Carranza et al. 2007; Swarup et al. 2008). Auxin also plays a role in this process and was recently reported to induce CWR genes and therefore facilitating cell wall separation (Swarup et al. 2008). SHY2/IAA3 was shown to mediate auxin response in the endodermis while the SLR/IAA14 / ARF7-ARF19 module induces expression of LAX3 in the cortex and the epidermis (Tian and Reed 1999; Swarup et al. 2008). The expression of the LAX3 auxin influx carrier protein consequently increases the auxin concentration in the cortex, and later in the epidermis, in turn inducing CWR genes and facilitating primordium outgrowth.

The activation of the meristem hallmarks the transition between the primordium and a lateral root growing autonomously. It occurs during or soon after the protrusion through the epidermal layer. The importance of auxin homeostasis was again shown through the characterization of mutants. A mutation in the gene ALF3 (ABERRANT LATERAL ROOT FORMATION 3) arrests lateral root growth soon after emergence but can be rescued by exogenous auxin application (Celenza et al. 1995). Mutation in the gene MDR1 (MULTIDRUG RESISTANCE 1) impairs acropetal transport of auxin and causes reduced elongation and/or arrest of the lateral roots (Wu et al. 2007). Taken together, these observations indicate a step at which the lateral root becomes more, but not fully, independent from the primary root for the auxin supply necessary for its growth and elongation.

Rise of New Technologies to Understand Lateral Root Development

Inducing LRI

The problem of the discreteness of the LRI events along the main root could firstly be circumvented by the use of a combination of treatments: the plants are first grown on a medium containing NPA, which inhibits auxin transport, and later transferred to a medium containing 1-naphthaleneacetic acid, which synchronously and homogeneously induces LRI in the entire pericycle of Arabidopsis seedlings (Himanen et al. 2002). The LRIS was used in different transcriptomics experiments (Himanen et al. 2004; Vanneste et al. 2005; De Smet et al. 2007). However, a limit of this system is the use of auxin treatments, which trigger vast and pleiotropic changes in gene expression. This limitation could be elegantly bypassed by applying the same treatment to the mutant slr-1 that does not form lateral roots under these conditions, in parallel to the wild-type plant, thus allowing the distinction of specific LRI genes from general auxin response pathways (Vanneste et al. 2005). In addition, chemical genomics, which makes use of small chemical compounds that can potentially interfere with metabolic pathways in planta allowed the discovery of new molecules capable of inducing LRI with a narrower effect on global gene expression (De Rybel et al. 2010a). Applied to the LRIS, such molecules should greatly help in deciphering the core pathways necessary and sufficient for LRI.

Mechanical external factors such as gravistimulation or bending of the root also induce LRI, on the external side of the bend (Ditengou et al. 2008; Lucas et al. 2008a; Richter et al. 2009). Upon gravistimulation, the differential redistribution of auxin fluxes in the root tip creates an auxin maximum in the lower side of the root tip, inhibiting cell elongation and triggering a bend bringing the root tip back in the direction of the gravity vector (Ottenschlager et al. 2003; Swarup et al. 2005). Meanwhile, PIN relocation at the convex side results in an auxin maximum in the protoxylem cells, which can be the cause of LRI (Ditengou et al. 2008). During mechanical bending, it is hypothesized that the stretching of the cells results in cytoplasmic increases of Ca2+, which in turns induces LRI (Richter et al. 2009). The possibility to synchronously induce LRI on a large population of plants by reorientation of the growing plates (i.e., gravistimulation) opens new perspectives for developmental studies. Among other possibilities, it will allow the production of transcriptome datasets following lateral root formation, from the initiation and through its development, without interfering massively with auxin pathways (Middleton et al. 2011).

Spatiotemporal Maps of Cell Types and Developmental Zones

A spatiotemporal gene expression map of individual root cell types and developmental zones in Arabidopsis was constructed by combining the use of tissue-specific marker lines with cell sorting (Birnbaum et al. 2005; Nawy et al. 2005; Lee et al. 2006; Brady et al. 2007). For the first time, these datasets made it possible to get precise in silico root expression profiles for a high number of genes. Furthermore, different studies can be envisaged based on tissue specificity, on radial and longitudinal expression patterns, and allow the construction of networks based on a combination of these observations (Brady et al. 2011). Cell sorting is however not easily transposable to all species, particularly due to the lack of tissue-specific marker lines but also due to the difficulties to prepare protoplasts of plants with a high number of cell layers and secondary cell wall thickening. This problem can be circumvented by using micro-dissection or LCM (Nelson et al. 2006; Ithal et al. 2007; Nelson et al. 2008). Different studies took profit of such approaches, with various degrees of resolution. In rice, the transcriptome of different cell types was analyzed throughout the plant (Jiao et al. 2009) and was recently ameliorated using better defined datasets specific for the root (Takehisa et al. 2012). The possibility to compare these transcriptome data between two different species provides the possibility, with an amelioration of the resolution for the root tissues, to isolate common regulatory genes responsible for changes in root architecture (Wang et al. 2010a).

Other studies comprising the root have been realized with a lower degree of resolution. These studies however contain information that can be valuable to increase our knowledge on primary and lateral root development. Transcriptome atlases have been realized in other monocotyledonous plants such as barley and maize (Druka et al. 2006; Sekhon et al. 2011) and also in dicotyledonous plants such as soybean and medicago (Benedito et al. 2008; Libault et al. 2010; Severin et al. 2010), which presents the advantage to contain different stages of nodulation, a process that can be compared to LRI and development (Mathesius et al. 2000). In addition, recent studies have taken advantage of this strategy and implemented the measurement of other regulatory mechanisms of gene expression, reflected in translatome, proteome, and metabolome analyses (Mustroph et al. 2009; Petersson et al. 2009; Matsuda et al. 2010).

ComparativOmics, the Future

While the importance of roots for nutrient acquisition and growth in crops is becoming increasingly clear, the molecular processes of LRI and development are very poorly understood in these species and remain mostly restricted to the model plant Arabidopsis (Den Herder et al. 2010; Gewin 2010). LRI is the major mechanism shared by angiosperms to control their root architecture. Consequently, it is very likely that it evolved from endogenous pathways present in a common ancestor and remained conserved throughout evolution. The conservation of gene families for which a role in LRI is known, among other anatomical and physiological observations, supports this theory (Table 1.2; Grunewald et al. 2007; Lau et al. 2008; Movahedi et al. 2011; Van Bel et al. 2012). Nevertheless, it is unclear whether orthology retained functionality through evolution. Genome duplication events and adaptation to environmental conditions may actually have led to gene diversity that highly complicates the task of looking for functional homologs only based on phylogenetic approaches (Van de Peer et al. 2009). In consequence, it is very complicated to define relevant orthologous genes from one species to another.

A lot of datasets have been generated during the last decade, which are directly or indirectly related to LRI (Table 1.2). In Arabidopsis, an effort to rationalize datasets together, in a compendium made accessible for the scientific community, allowed the discovery of new key regulators (De Rybel et al. 2010b; Parizot et al. 2010) and the generation of multiple networks (Lee et al. 2010; Brady et al. 2011). The possibility to compare the involvement of genes in different processes and in different species may allow to draw a link between orthologs and highlight the importance to realize “omics” studies in different species (Galbraith and Edwards 2010). A comparison of the transcriptional atlases in Arabidopsis and poplar already indicated the possibility to study organ-specific orthologs (Quesada et al. 2008). In this perspective, the rise of new sequencing technologies will be of great help in transferring root genomics knowledge to crop species (Varshney et al. 2009).

Acknowledgments

This work was supported by a grant from the Interuniversity Attraction Poles Programme (IAP VII/29), initiated by the Belgium Science Policy Office. Boris Parizot is supported by the Research Foundation Flanders (FWO, grant 3G002911). We thank Marlies Demeulenaere for comments that greatly improved the manuscript.

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